Updated: Tue Jan 19 17:22:10 2016
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| ## Candidates ### Figure S1b: UMR asymmetry * UMRs frequency (bp/MB) for each chromosome for MeDIP UMRs between MZ twins |
| ### Figure S1c: UMR locations * Locations of UMRs along each chromosome for MeDIP UMRs between MZ twins |
| ### Figure S1g: miRNA * Heatmap of differential expressed and highly expressed (RPM > 100) miRNAs between MZ twins |
| ### Figure S2a: UMR asymmetry |
| ### Figure S2b: UMR locations * Locations of UMRs along each chromosome for WGBS UMRs between cortex and GE NPCs |
| ### Figure S2c: UMR genomic breakdown * Fold enrichment on log2 scale for overlapping genomic regions with WGBS UMRs between cortex and GE NPCs |
| ### Figure S2f: miRNA * (A). Unique miRNA detected (>0.1 reads per million mapped) across all samples. Heatmap of differential expressed and highly expressed (RPM > 100) miRNAs between MZ twins (B), cortex and GE NPCs (C), and gestational weeks (D). |
| ### Figure S3a: UMR asymmetry * UMRs frequency (bp/MB) for each chromosome for WGBS UMRs between GW13 and GW17 |
| ### Figure S3b: UMR locations * Locations of UMRs along each chromosome for WGBS UMRs between GW13 and GW17 |
| ### Figure S3c: UMR genomic breakdown * Fold enrichment on log2 scale for overlapping genomic regions with WGBS UMRs between GW13 and GW17 |
| ### Figure S5b: Venn diagram of differential expressed genes between GW |
| * Venn diagrame of No. of differential expressed genes between different gestational weeks |
| ### Figure S5c: DAVID enrichment for DE genes |
| * DAVID GO biological processes enriched for DE genes between gestational weeks |
| ### Figure S5d: DAVID enrichment for isoform genes |
| * DAVID enriched terms (FDR < 0.01) for isoforms across gestational weeks |
| ### Figure S5e: miRNA |
| * Heatmap of differential expressed and highly expressed (RPM > 100) miRNAs between gestational weeks |
| ### Supplemental 11: Fraction of DE genes with proximal UMRs |
| * Fraction of differential expressed genes proximally (TSS +/- 1500bp) associated with MeDIP UMRs between MZ twins (A), WGBS UMRs between cortex and GE NPCs (B), and WGBS UMRs between GW13 and GW17 (C). |
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| ### Supplemental 12: TFBS asymmetry between neurosphere UMRs |
| * Relative abundance of transcription factor binding sites overlapping UMRs in NPCs cortex and GE cells reveals regulatory asymmetry between cell types. Red represents transcription factor more enriched in cortex, and blue represents transcription factor enriched in GE. |
| ### Supplemental 14: Expression of DNA methylation reulators |
| * Heatmap of RPKM for DNA methylation regulators across all samples. |
| ### Supplemental 16: Correlating histone modifications with transcription |
| * Divide genes into 8 groups according to whether their genebody are marked by H3K36me3 (top panel: marked, bottom panel: not marked), and whether their promoters are marked by H3K4me3 and H3K27me3 (panels from left to right: marked by H3K4me3 only, both, H3K37me3 only, neither), and plot boxplot of gene RPKM on the log10 scale (RPKM < 0.005 are set to 0.005). |
| ### Supplemental 17: DNA methylation at exon boundaries |
| * Exon-intron junction mCpGs provide an inherited signature of exon expression. Average number of CpGs (black, bottom panel) and average mCpG levels (whole genome bisulfite shotgun, 20bp bins) at exon junctions +/- 200bp in cortex (solid line with round dots) and GE (dashed line with triangles). Exons are divided into four groups: 1) exons expressed in both cell types (exon RPKM > 0.1 in cortex and GE, purple); 2) cortex-specific exons (isoform exons expressed in cortex but not in GE, red); 3) GE-specific exons (isoform exons expressed in GE but not in cortex, green), and 4) exons not expressed in either cell types (all other exons, blue). |
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| ### Supplemental 18: Neurosphere UMR enrichemnt at chromosome ends |
| * Fraction of UMRs along normalized length of the genome in cortex and GE specific UMRs (A), and GW specific UMRs (B). |
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| ### Supplemental 19: TFBS asymmetry in GW UMRs |
| * Relative abundance of transcription factor binding sites overlapping UMRs between gestational weeks. |